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- PDB-2om2: Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif O... -

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Basic information

Entry
Database: PDB / ID: 2om2
TitleCrystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
Components
  • Guanine nucleotide-binding protein G(i), alpha-1 subunit
  • Regulator of G-protein signalling 14 GoLoco motif peptide
KeywordsSIGNALING PROTEIN / Arginine finger / RGS14 GoLoco
Function / homology
Function and homology information


zygote asymmetric cell division / negative regulation of synaptic plasticity / regulation of G protein-coupled receptor signaling pathway / GTPase activating protein binding / positive regulation of neurogenesis / GDP-dissociation inhibitor activity / nucleocytoplasmic transport / spindle organization / negative regulation of G protein-coupled receptor signaling pathway / platelet-derived growth factor receptor signaling pathway ...zygote asymmetric cell division / negative regulation of synaptic plasticity / regulation of G protein-coupled receptor signaling pathway / GTPase activating protein binding / positive regulation of neurogenesis / GDP-dissociation inhibitor activity / nucleocytoplasmic transport / spindle organization / negative regulation of G protein-coupled receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / negative regulation of MAP kinase activity / G-protein alpha-subunit binding / long-term memory / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / Adenylate cyclase inhibitory pathway / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / adenylate cyclase regulator activity / G protein-coupled serotonin receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / cellular response to forskolin / GTPase activator activity / regulation of mitotic spindle organization / learning / chromosome segregation / Regulation of insulin secretion / positive regulation of cholesterol biosynthetic process / negative regulation of insulin secretion / G protein-coupled receptor binding / response to peptide hormone / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / PML body / visual learning / negative regulation of ERK1 and ERK2 cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / centriolar satellite / spindle / long-term synaptic potentiation / spindle pole / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / GDP binding / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / heterotrimeric G-protein complex / mitotic cell cycle / signaling receptor complex adaptor activity / G protein activity / response to oxidative stress / midbody / cell cortex / G alpha (i) signalling events / G alpha (s) signalling events / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / dendritic spine / microtubule / Extra-nuclear estrogen signaling / postsynaptic density / nuclear body / ciliary basal body / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / dendrite / centrosome / protein kinase binding / GTP binding / nucleolus / glutamatergic synapse / magnesium ion binding / Golgi apparatus / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
RGS14, RGS domain / : / : / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / RGS, subdomain 1/3 / GI Alpha 1, domain 2-like ...RGS14, RGS domain / : / : / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / RGS, subdomain 1/3 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Regulator of G-protein signaling 14 / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Regulator of G-protein signaling 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSiderovski, D.P. / Kimple, R.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure-based Protocol for Identifying Mutations that Enhance Protein-Protein Binding Affinities.
Authors: Sammond, D.W. / Eletr, Z.M. / Purbeck, C. / Kimple, R.J. / Siderovski, D.P. / Kuhlman, B.
History
DepositionJan 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(i), alpha-1 subunit
B: Regulator of G-protein signalling 14 GoLoco motif peptide
C: Guanine nucleotide-binding protein G(i), alpha-1 subunit
D: Regulator of G-protein signalling 14 GoLoco motif peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4418
Polymers82,5064
Non-polymers9354
Water5,152286
1
A: Guanine nucleotide-binding protein G(i), alpha-1 subunit
B: Regulator of G-protein signalling 14 GoLoco motif peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7204
Polymers41,2532
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-33 kcal/mol
Surface area16150 Å2
MethodPISA
2
C: Guanine nucleotide-binding protein G(i), alpha-1 subunit
D: Regulator of G-protein signalling 14 GoLoco motif peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7204
Polymers41,2532
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-36 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.592, 82.311, 187.566
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Guanine nucleotide-binding protein G(i), alpha-1 subunit / Adenylate cyclase-inhibiting G alpha protein


Mass: 37159.348 Da / Num. of mol.: 2 / Fragment: G{alpha}i1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Plasmid: pPROEX Htb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P63096
#2: Protein/peptide Regulator of G-protein signalling 14 GoLoco motif peptide


Mass: 4093.621 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence occurs naturally in Homo sapiens (human).
References: UniProt: Q506M1, UniProt: O43566*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.55M Ammonium Sulfate, 100 mM Sodium Acetate pH 5.0, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 55498 / Num. obs: 55436 / % possible obs: 99.9 %

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KJY

1kjy


Resolution: 2.2→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.26 5627 10.1 %
Rwork0.227 --
obs-55436 99.9 %
Solvent computationBsol: 44.552 Å2
Displacement parametersBiso mean: 41.252 Å2
Baniso -1Baniso -2Baniso -3
1-3.569 Å20 Å20 Å2
2---2.612 Å20 Å2
3----0.956 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5695 0 58 286 6039
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.13
X-RAY DIFFRACTIONc_mcbond_it1.5771.5
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_mcangle_it2.6362
X-RAY DIFFRACTIONc_scangle_it3.1612.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4gdp.paramgdp.top

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